We study the electron transport through pi-stacked structures bound to metallic electrodes and in particular examine both the energy dependence and the effect of spatial dislocations on the electronic transmission We compare these results with the predictions that can be made regarding the behavior of these systems from a model of the electronic coupling matrix elements derived from the splitting of monomer molecular orbitals in the dimer structure We show that whereas these models agree reasonably well for predictions of near-resonant transport in a small stack of substituted benzene molecules, the relationship between these two approaches is less clear in larger structures where the mechanisms and pathways can become more complex